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- PDB-6qbl: NMR Structure of Big-defensin 1 from oyster Crassostrea gigas -

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Basic information

Entry
Database: PDB / ID: 6qbl
TitleNMR Structure of Big-defensin 1 from oyster Crassostrea gigas
ComponentsBig defensin 1
KeywordsANTIMICROBIAL PROTEIN / Big-defensin / antimicrobial / marine / oyster / salt insensitive activity
Function / homologyBig defensin / Myotoxin/Anemone neurotoxin domain superfamily / membrane / Big defensin 1
Function and homology information
Biological speciesCrassostrea gigas (Pacific oyster)
MethodSOLUTION NMR / simulated annealing
AuthorsLoth, K. / Meudal, H. / Delmas, A.F.
CitationJournal: Mbio / Year: 2019
Title: The Ancestral N-Terminal Domain of Big Defensins Drives Bacterially Triggered Assembly into Antimicrobial Nanonets.
Authors: Loth, K. / Vergnes, A. / Barreto, C. / Voisin, S.N. / Meudal, H. / Da Silva, J. / Bressan, A. / Belmadi, N. / Bachere, E. / Aucagne, V. / Cazevielle, C. / Marchandin, H. / Rosa, R.D. / ...Authors: Loth, K. / Vergnes, A. / Barreto, C. / Voisin, S.N. / Meudal, H. / Da Silva, J. / Bressan, A. / Belmadi, N. / Bachere, E. / Aucagne, V. / Cazevielle, C. / Marchandin, H. / Rosa, R.D. / Bulet, P. / Touqui, L. / Delmas, A.F. / Destoumieux-Garzon, D.
History
DepositionDec 21, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 11, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2025Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Big defensin 1


Theoretical massNumber of molelcules
Total (without water)10,7131
Polymers10,7131
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area250 Å2
ΔGint0 kcal/mol
Surface area5530 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 150total energies and restraint violation statistics
RepresentativeModel #1lowest energy

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Components

#1: Protein Big defensin 1


Mass: 10712.988 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Crassostrea gigas (Pacific oyster) / References: UniProt: F6M2J2
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-1H TOCSY
121isotropic12D 1H-1H NOESY
131isotropic12D 1H-15N HSQC
141isotropic12D 1H-13C HSQC

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Sample preparation

DetailsType: solution / Contents: 1.0 mM [1-93]Cg-BigDef1, 90% H2O/10% D2O / Label: unlabelled / Solvent system: 90% H2O/10% D2O
SampleConc.: 1.0 mM / Component: [1-93]Cg-BigDef1 / Isotopic labeling: natural abundance
Sample conditionsIonic strength: 0 mM / Label: conditions_1 / pH: 4.6 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III HD / Manufacturer: Bruker / Model: AVANCE III HD / Field strength: 700 MHz / Details: cryoprobe

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Processing

NMR software
NameDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
ARIALinge, O'Donoghue and Nilgesstructure calculation
CcpNmr AnalysisCCPNchemical shift assignment
CcpNmr AnalysisCCPNpeak picking
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: total energies and restraint violation statistics
Conformers calculated total number: 150 / Conformers submitted total number: 10

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